Alignments for a candidate for nagF in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Marinobacter adhaerens HP15

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate GFF3781 HP15_3723 PTS system, glucose-specific EIIA/HPr/phosphoenolpyruvate-protein phosphotransferase components

Query= reanno::BFirm:BPHYT_RS02740
         (854 letters)



>FitnessBrowser__Marino:GFF3781
          Length = 978

 Score =  452 bits (1164), Expect = e-131
 Identities = 303/738 (41%), Positives = 408/738 (55%), Gaps = 31/738 (4%)

Query: 123 VSVIAIANSDAFEIVERVQGGLLKAGETPLLVLRARDGAAAEASRQLSSTNVTEEARQQV 182
           V  +A    +  +++ER+   L  AG+ P+       G +AEA     S    +    +V
Sbjct: 263 VFCLAGPGDECHDLLERIDTFL--AGDEPI------QGLSAEALLARLSGEAADAVTAKV 314

Query: 183 TLVHAGGLHARPAARAREAARGFDARVEVRY-EGRKAAIE--SVVGLLGLGAGEGATVEL 239
           TL++  GLHARPA +  + AR  +A + +R  EG  AA+   S+  ++GLGA  G T+ L
Sbjct: 315 TLLNTHGLHARPAKQLVQEARRHNASIRLRLLEGEGAAVSATSLTRVIGLGARRGQTLLL 374

Query: 240 LGMGPQAAAAVAAIANELTREAHGEVEEK--PARQSSP---APQAVARPAGETLAPNTLA 294
              G  A+ A+ +    LT    G + EK  P R + P    P+A   PA     P  + 
Sbjct: 375 SATGDDASQAIQS----LTSAIEGGLGEKVSPLRSADPQTKVPEAEQAPALTDDQP--VK 428

Query: 295 GVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRG 354
            V A+PG+A+          ++ P+ A  +     RL ++A+ + D  L T +R A    
Sbjct: 429 AVAASPGLALAPAFVMRQPTLEYPQFAEDSEQQIQRL-NQAVDSADGQLRTLIRQAEGGE 487

Query: 355 AVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAER 414
           A   A I SVH  +L+D  L  A  + I+ G SA   W +AI         + D LLAER
Sbjct: 488 A---APILSVHVEMLQDEDLYQATLEAINEGASAEAGWWKAIDTAARGQEALADRLLAER 544

Query: 415 AADLRDIEKRVLRAL-GYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTALVMARGGA 473
           AADLRD+ +RVL  L G    T    P   +L A++  PSD++ LD +RV  LV ARGGA
Sbjct: 545 AADLRDVGRRVLSNLCGVAMPTPPDTPY--ILVADDLGPSDVARLDTTRVRGLVTARGGA 602

Query: 474 TSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRL 533
           TSH+AILAR  G+PA+V  G+ +  I  G+ +VV+   G L   P     E+ R    +L
Sbjct: 603 TSHSAILARALGLPAVVGTGERILTILNGSDLVVDGERGCLVPNPGAERCEKIRRRLQQL 662

Query: 534 ADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAA 593
             ++        Q A T DG  IEV AN+        AVE GAD VGLLRTE +F+    
Sbjct: 663 DALQAEAHENRNQPATTVDGHTIEVCANLGNTAHTPDAVERGADGVGLLRTEFIFMAHPE 722

Query: 594 APTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVR 653
           AP        YQ   DAL+G   + RTLDVG DK +DY  LP E NP LG+RGIRL+  R
Sbjct: 723 APDLATQVTEYQHAFDALNGLPLVARTLDVGGDKPLDYWPLPQEDNPFLGMRGIRLSLTR 782

Query: 654 PDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIE 713
           PD+L+ Q+R LL       +RI+ PMV D+ E    R  + +   E+  +  ++VGVMIE
Sbjct: 783 PDILETQVRALLTAAGDRPLRIMFPMVKDLEEFRAARAIVTKVQSEVSASN-VQVGVMIE 841

Query: 714 VPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQG 773
           VPS ALLA  LA   DF SIGTNDLTQYTLA+DR    L+A++DGLHP+VLRLI  TV+ 
Sbjct: 842 VPSCALLASTLAPEVDFFSIGTNDLTQYTLAIDRGHGQLSAESDGLHPSVLRLIRMTVEA 901

Query: 774 ADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQD 833
           A  H +WVGVCG LA DP A+P+LVGL V ELSV    VP +KA +R L+ +  RQ+A+ 
Sbjct: 902 AHAHNRWVGVCGELASDPQAIPVLVGLDVDELSVTSRRVPLVKACIRGLNLENARQQAEK 961

Query: 834 ALALESAQAVRAASRETW 851
           AL+L +A  VR A  E W
Sbjct: 962 ALSLATASEVRDA-LEAW 978


Lambda     K      H
   0.317    0.133    0.371 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1758
Number of extensions: 87
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 854
Length of database: 978
Length adjustment: 43
Effective length of query: 811
Effective length of database: 935
Effective search space:   758285
Effective search space used:   758285
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources